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- PDB-4uha: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 4uha
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)-5-(methyl(2-(methylamino)ethyl)amino)benzonitrile
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / mitochondrion organization / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-Q1T / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J. Med. Chem. / Year: 2015
Title: 2-Aminopyridines with a Truncated Side Chain To Improve Human Neuronal Nitric Oxide Synthase Inhibitory Potency and Selectivity.
Authors: Kang, S. / Li, H. / Tang, W. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionMar 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 2.0Jan 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / exptl_crystal_grow / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.formula_weight / _entity.pdbx_description / _exptl_crystal_grow.method / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
B: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,30215
Polymers99,4542
Non-polymers2,84813
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-124 kcal/mol
Surface area31980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.959, 106.300, 156.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE, ENDOTHELIAL / CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL ...CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL NITRIC OXIDE SYNTHASE


Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 40-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 246 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-Q1T / 3-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL)-5-(METHYL(2-(METHYLAMINO)ETHYL)AMINO)BENZONITRILE


Mass: 323.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N5
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsS-(DIMETHYLARSENIC)CYSTEINE (CAS): A MODIFIED CYS RESIDUE
Sequence detailsRESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 % / Description: RMERGE 1.741 RPIM 1.531 CC ONE HALF 0.346
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 20-22% PEG3350 0.1M CACODYLATE, PH6.0 140-200 MM MG ACETATE 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49840 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 45.86 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→39.173 Å / SU ML: 0.39 / σ(F): 1.11 / Phase error: 28.81 / Stereochemistry target values: ML
Details: RESIDUES 109 TO 120 IN CHAIN A AND 110 TO 120 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2398 4668 5 %
Rwork0.1807 --
obs0.1836 49581 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 197 233 6854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086809
X-RAY DIFFRACTIONf_angle_d1.2019295
X-RAY DIFFRACTIONf_dihedral_angle_d16.0932451
X-RAY DIFFRACTIONf_chiral_restr0.072968
X-RAY DIFFRACTIONf_plane_restr0.0051197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.22520.43081540.40442632X-RAY DIFFRACTION88
2.2252-2.25130.40021390.37222926X-RAY DIFFRACTION97
2.2513-2.27880.43551510.36932875X-RAY DIFFRACTION97
2.2788-2.30760.4511280.35552988X-RAY DIFFRACTION97
2.3076-2.3380.3711560.34652966X-RAY DIFFRACTION99
2.338-2.370.39281720.32472905X-RAY DIFFRACTION98
2.37-2.40390.36461530.31662973X-RAY DIFFRACTION99
2.4039-2.43970.36011550.30192944X-RAY DIFFRACTION99
2.4397-2.47790.32651680.28562952X-RAY DIFFRACTION99
2.4779-2.51850.34031810.27192989X-RAY DIFFRACTION99
2.5185-2.56190.34931680.2592913X-RAY DIFFRACTION99
2.5619-2.60850.28451700.24222954X-RAY DIFFRACTION99
2.6085-2.65860.29691550.242976X-RAY DIFFRACTION99
2.6586-2.71290.29121500.22562975X-RAY DIFFRACTION99
2.7129-2.77190.27731560.23242977X-RAY DIFFRACTION99
2.7719-2.83630.3611120.22712981X-RAY DIFFRACTION99
2.8363-2.90720.30891500.20753037X-RAY DIFFRACTION99
2.9072-2.98580.26171580.18612895X-RAY DIFFRACTION99
2.9858-3.07360.2311760.17782997X-RAY DIFFRACTION99
3.0736-3.17280.25421470.17752964X-RAY DIFFRACTION99
3.1728-3.28610.26831510.18533009X-RAY DIFFRACTION99
3.2861-3.41760.26331700.16832967X-RAY DIFFRACTION99
3.4176-3.57310.20691450.1572961X-RAY DIFFRACTION99
3.5731-3.76130.21461640.13892950X-RAY DIFFRACTION99
3.7613-3.99680.191480.13862991X-RAY DIFFRACTION99
3.9968-4.3050.1691570.12842972X-RAY DIFFRACTION99
4.305-4.73760.161610.11532982X-RAY DIFFRACTION99
4.7376-5.42160.21981260.12982992X-RAY DIFFRACTION99
5.4216-6.82470.19271680.15752965X-RAY DIFFRACTION99
6.8247-39.17890.19561790.15362959X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.7617 Å / Origin y: 8.1469 Å / Origin z: 49.5649 Å
111213212223313233
T0.1577 Å2-0.0286 Å2-0.0055 Å2-0.2206 Å20.001 Å2--0.2605 Å2
L0.3121 °20.1342 °2-0.1783 °2-1.15 °20.084 °2--1.7372 °2
S0.0305 Å °-0.0593 Å °-0.0338 Å °-0.0741 Å °0.0392 Å °-0.1634 Å °-0.0712 Å °0.0981 Å °-0.0482 Å °
Refinement TLS groupSelection details: ALL

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